Question: How to fill in missing fields on a VCF to convert into a genotype matrix?
0
gravatar for jespinoz
2.0 years ago by
jespinoz20
jespinoz20 wrote:

My VCF file looks like the screenshot below and I believe it is missing the necessary fields to convert it into a genotype matrix that I can actually use. It's 14GB and contains 88 samples.

How can I fill the missing fields (e.g. GT) and convert it into a genotype matrix with exact commands?

I've found references for similar questions that are one sentence answers with a link to a tool but many issues aren't addressed and I have yet to find a good tutorial on how to fill in missing fields on a VCF file and convert it to genotype/SNPs matrix.

Thank you : )

enter image description here

genotype bcf snps matrix vcf • 797 views
ADD COMMENTlink written 2.0 years ago by jespinoz20

My first guess: those are probably missing because they weren't genotyped.

ADD REPLYlink written 2.0 years ago by WouterDeCoster39k

I used samtools mpileup. How can I genotype them? I have all of the bam files still.

ADD REPLYlink written 2.0 years ago by jespinoz20

You could check for one of the missing samples if that position is covered in your bam file.

ADD REPLYlink written 2.0 years ago by WouterDeCoster39k
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